Non-standard fields are assumed to be responsible for phenomena attributed to dark energy and dark matter. Being coupled to ordinary matter, these fields modify the masses and/or charges of the elementary particles, thereby violating the Weak Equivalence Principle. Thus, values of fundamental constants such as the proton-to-electron mass ratio, mu, and/or the fine structure constant, alpha, measured in different environment conditions can be used as probes for this coupling. Here we perform differential measurements of F = mu*alpha^2 to test a non-standard coupling in the Magellanic Clouds - dwarf galaxies where the overall mass budget is dominated by dark matter. The analysis is based on [CI] and CO lines observed with the Herschel Space Observatory. Since these lines have different sensitivities to changes in mu and alpha, the combined alpha and mu variations can be evaluated through the radial velocity offsets, Delta V, between the CO and [CI] lines. Averaging over nine positions in the Magellanic Clouds, we obtain <Delta V> = -0.02+/-0.07 km/s, leading to |Delta F/F| < 2*10^-7 (1sigma), where Delta F/F = (F_obs-F_lab)/F_lab}. However, for one position observed with five times higher spectral resolution we find Delta V = -0.05+/-0.02 km/s, resulting in Delta F/F = (-1.7+/-0.7)*10^-7. Whether this offset is due to changes in the fundamental constants, due to chemical segregation in the emitting gas or merely due to Doppler noise requires further investigations.